JAL-1953 2.11.2 with Archeopteryx!

[jalview.git] / src / jalview / ext / archaeopteryx / LoadedTreeAssociation.java

diff --git a/src/jalview/ext/archaeopteryx/LoadedTreeAssociation.java b/src/jalview/ext/archaeopteryx/LoadedTreeAssociation.java
deleted file mode 100644 (file)
index c869cd5..0000000
--- a/src/jalview/ext/archaeopteryx/LoadedTreeAssociation.java
+++ /dev/null
@@ -1,163 +0,0 @@
-package jalview.ext.archaeopteryx;
-
-import jalview.analysis.SequenceIdMatcher;
-import jalview.datamodel.SequenceI;
-import jalview.ext.forester.DataConversions;
-import jalview.ext.treeviewer.ExternalLoadedTreeAssociationI;
-import jalview.util.MappingUtils;
-
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import org.forester.phylogeny.Phylogeny;
-import org.forester.phylogeny.PhylogenyNode;
-
-public class LoadedTreeAssociation
-        implements ExternalLoadedTreeAssociationI
-{
-  SequenceI[] alignSequences;
-
-  Phylogeny tree;
-
-  Map<SequenceI, PhylogenyNode> alignmentWithNodes;
-
-  Map<PhylogenyNode, SequenceI> nodesWithAlignment;
-
-  public LoadedTreeAssociation(SequenceI[] alignmentSequences,
-          Phylogeny aptxTree)
-  {
-    alignSequences = alignmentSequences;
-    tree = aptxTree;
-    alignmentWithNodes = new HashMap<>(alignSequences.length);
-    nodesWithAlignment = new HashMap<>(alignSequences.length);
-
-  }
-
-
-
-  /**
-   * Tries to match sequences from Jalview with tree nodes in Archaeopteryx and
-   * fills in the tree node with sequence data if a match is found.
-   * 
-   * Partially refactored from the old Jalview TreeModel
-   * associateLeavesToSequences method.
-   *
-   * @param seqs
-   * @param aptxTree
-   */
-  @Override
-  public void associateLeavesToSequences()
-
-  {
-    SequenceIdMatcher algnIds = new SequenceIdMatcher(alignSequences);
-
-    List<PhylogenyNode> leaves = tree.getExternalNodes();
-    SequenceI nodeSequence;
-    String nodeSequenceName;
-
-    for (PhylogenyNode treeNode : leaves)
-    {
-      nodeSequenceName = treeNode.getName();
-
-      nodeSequence = algnIds.findIdMatch(nodeSequenceName);
-      if (nodeSequence != null)
-      {
-        org.forester.phylogeny.data.Sequence foresterNodeSeq = DataConversions
-                .createForesterSequence(nodeSequence, true);
-        treeNode.getNodeData().setSequence(foresterNodeSeq);
-
-        MappingUtils.putWithDuplicationCheck(alignmentWithNodes,
-                nodeSequence, treeNode);
-        MappingUtils.putWithDuplicationCheck(nodesWithAlignment,
-                treeNode, nodeSequence);
-
-
-      }
-
-    }
-
-  }
-
-
-
-  public Map<SequenceI, PhylogenyNode> getAlignmentWithNodes()
-  {
-    return alignmentWithNodes;
-  }
-
-  public Map<PhylogenyNode, SequenceI> getNodesWithAlignment()
-  {
-    return nodesWithAlignment;
-  }
-
-  // {
-  // SequenceIdMatcher algnIds = new SequenceIdMatcher(seqs);
-  //
-  // List<PhylogenyNode> leaves = aptxTree.getExternalNodes();
-  //
-  // int namesleft = seqs.length;
-  // SequenceI nodeSequence;
-  // String nodeSequenceName;
-  // List<SequenceI> one2many = new ArrayList<>();
-  // int countOne2Many = 0;
-  //
-  // for (PhylogenyNode treeNode : leaves)
-  // {
-  // nodeSequenceName = treeNode.getName();
-  // nodeSequence = null;
-  //
-  // if (namesleft > -1)
-  // {
-  // nodeSequence = algnIds.findIdMatch(nodeSequenceName);
-  // }
-  //
-  // if (nodeSequence != null)
-  // {
-  // org.forester.phylogeny.data.Sequence foresterNodeSeq =
-  // ForesterDataConversions.createForesterSequence(nodeSequence, true);
-  //
-  // treeNode.getNodeData().setSequence(foresterNodeSeq);
-  // if (one2many.contains(nodeSequence))
-  // {
-  // countOne2Many++;
-  // if (jalview.bin.Cache.log.isDebugEnabled())
-  // {
-  // jalview.bin.Cache.log.debug("One 2 many relationship for"
-  // +nodeSequence.getName());
-  // }
-  // }
-  // else
-  // {
-  // one2many.add(nodeSequence);
-  // namesleft--;
-  // }
-  // }
-  // else
-  // {
-  // treeNode.setCollapse(true); // collapse nodes that couldn't be connected
-  // // to a sequence
-  //
-  //
-  // // treeNode.setElement( new Sequence(nodeSequenceName,
-  // "THISISAPLACEHOLDER"));
-  // // treeNode.setPlaceholder(true);
-  // }
-  // }
-  // if (jalview.bin.Cache.log.isDebugEnabled() && countOne2Many > 0)
-  // {
-  // jalview.bin.Cache.log.debug("There were " + countOne2Many
-  // + "alignment sequence ids (out of" + one2many.size()
-  // + " unique ids) linked to two or more leaves.");
-  // }
-  // one2many.clear();
-  //
-  // }
-
-}
-
-
-
-
-
-